From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jun 15 2006 - 16:06:09 CDT
this is most likely a problem with your periodic cell being too small.
You need to set the cell basis vectors such that they fully enclose your
system, and the center to be the geometric center of your system (vmd's
measure minmax and measure center commands are very helpful here). What
is the size of the cell you used, and how big is your system?
Moumita Maiti wrote:
> I have a molecule which consists of 267224 atoms. I gives
> the following error(pasted at the end of the text) when I run conf
> file with namd2.
> I have two questions:
> 1. Is there a possibility that the problem is with psf file? I had
> some warnings about some of the atoms when it was trying to guess the
> coordinates for those.
> 2. I used 310K temperature and the other parameters like pirlist dist,
> electrostatics..etc, just the values which were in the exaple file
> "ubq_wb_eq.conf" of the tutorial.
> 3. How do you decide the periodic boundary values?
> I understand some term is becoming infinity, I want to know the
> possibilities which can cause this type of problem.
> The error is:
> PRESSURE: 0 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
> ENERGY: 0 93111.2340 -99999999.9999 13742.5589
> 18.4616 -2425107.4313 99999999.9999 0.0000
> 0.0000 0.0000 -99999999.9999 0.0000
> -99999999.9999 -99999999.9999 0.0000 -99999999.9999
> -99999999.9999 86856.0000 -99999999.9999 -99999999.9999
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
> Thank you,
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